pylocuszoom 0.2.0__tar.gz → 0.3.0__tar.gz

{pylocuszoom-0.2.0 → pylocuszoom-0.3.0}/CHANGELOG.md

@@ -5,7 +5,33 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [0.3.0] - 2026-01-26
+
+### Added
+- Bioconda recipe for conda installation
+- `adjustText` moved to default dependencies (was optional)
+- **Interactive plotly backend** - use `backend="plotly"` for hover tooltips and pan/zoom
+- **Interactive bokeh backend** - use `backend="bokeh"` for dashboard-ready plots
+
+### Changed
+- `plot()` and `plot_stacked()` now use backend protocol for all rendering (scatter, line, axes, layout)
+- **Gene track now works with all backends** (plotly, bokeh, matplotlib)
+- **Recombination overlay now works with all backends** - secondary y-axis with rate line and fill
+- **LD legend now works with all backends** - r² color scale (lead SNP highlighted in plot, not legend)
+- SNP labels remain matplotlib-only (interactive backends use hover tooltips instead)
+- Default `genomewide_threshold` changed from 5e-7 to 5e-8 (standard GWAS significance)
+- Gene track strand colors: forward strand now goldenrod (#DAA520), reverse strand light blue (#6BB3FF)
+- Gene track directional arrows: black for forward, dark grey for reverse
+- Added panel spacing (hspace=0.1) between stacked/fine-mapping panels for visual separation
+- Tightened gene track internal spacing for more compact layout
+
+### Fixed
+- Bokeh backend `x_range=None` error when creating figures with shared x-axis
+- Bokeh backend `legend_label=None` error in scatter plots
+- Bokeh backend LD legend not rendering (empty scatter plots don't create legend glyphs)
+- Bokeh backend deprecated `FuncTickFormatter` replaced with `CustomJSTickFormatter`
+- Bokeh backend deprecated `circle()` method replaced with `scatter(marker=...)`
+- Bokeh backend `FIXED_SIZING_MODE` validation warning in column layouts
 
 ## [0.2.0] - 2026-01-26
 
@@ -54,6 +80,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - bokeh >= 3.8.2
 - kaleido >= 0.2.0
 
-[Unreleased]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.2.0...HEAD
+[Unreleased]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.3.0...HEAD
+[0.3.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.2.0...v0.3.0
 [0.2.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v0.1.0...v0.2.0
 [0.1.0]: https://github.com/michael-denyer/pyLocusZoom/releases/tag/v0.1.0

{pylocuszoom-0.2.0 → pylocuszoom-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pylocuszoom
-Version: 0.2.0
+Version: 0.3.0
 Summary: Regional association plots for GWAS results with LD coloring, gene tracks, and recombination rate overlays
 Project-URL: Homepage, https://github.com/michael-denyer/pylocuszoom
 Project-URL: Documentation, https://github.com/michael-denyer/pylocuszoom#readme
@@ -19,6 +19,7 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.10
+Requires-Dist: adjusttext>=0.8
 Requires-Dist: bokeh>=3.8.2
 Requires-Dist: kaleido>=0.2.0
 Requires-Dist: loguru>=0.7.0
@@ -28,14 +29,11 @@ Requires-Dist: pandas>=1.4.0
 Requires-Dist: plotly>=5.0.0
 Requires-Dist: pyliftover>=0.4
 Provides-Extra: all
-Requires-Dist: adjusttext>=0.8; extra == 'all'
 Requires-Dist: pyspark>=3.0.0; extra == 'all'
 Provides-Extra: dev
 Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
 Requires-Dist: pytest>=7.0.0; extra == 'dev'
 Requires-Dist: ruff>=0.1.0; extra == 'dev'
-Provides-Extra: labels
-Requires-Dist: adjusttext>=0.8; extra == 'labels'
 Provides-Extra: spark
 Requires-Dist: pyspark>=3.0.0; extra == 'spark'
 Description-Content-Type: text/markdown
@@ -75,14 +73,20 @@ Inspired by [LocusZoom](http://locuszoom.org/) and [locuszoomr](https://github.c
 
 ## Installation
 
+```bash
+pip install pylocuszoom
+```
+
+Or with uv:
+
 ```bash
 uv add pylocuszoom
 ```
 
-Or with pip:
+Or with conda (Bioconda):
 
 ```bash
-pip install pylocuszoom
+conda install -c bioconda pylocuszoom
 ```
 
 ## Quick Start
@@ -165,20 +169,30 @@ fig = plotter.plot(
 )
 ```
 
-## Interactive Backends (Coming Soon)
+## Backends
 
-> **Note:** Interactive backends (plotly, bokeh) are planned but not yet fully integrated. Currently all plots use matplotlib.
+pyLocusZoom supports multiple rendering backends:
 
 ```python
-# Static publication-quality plot (default, currently only supported backend)
-plotter = LocusZoomPlotter(species="canine", backend="matplotlib")
-fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
+# Static publication-quality plot (default)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="matplotlib")
 fig.savefig("plot.png", dpi=150)
+
+# Interactive Plotly (hover tooltips, pan/zoom)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="plotly")
+fig.write_html("plot.html")
+
+# Interactive Bokeh (dashboard-ready)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="bokeh")
 ```
 
-Future releases will support:
-- **Plotly**: Interactive plots with hover tooltips, zoom/pan
-- **Bokeh**: Dashboard-friendly interactive plots
+| Backend | Output | Best For |
+|---------|--------|----------|
+| `matplotlib` | Static PNG/PDF/SVG | Publications, presentations |
+| `plotly` | Interactive HTML | Web reports, data exploration |
+| `bokeh` | Interactive HTML | Dashboards, web apps |
+
+> **Note:** All backends support gene track, recombination overlay, and LD legend. SNP labels (auto-positioned with adjustText) are matplotlib-only.
 
 ## Stacked Plots
 

{pylocuszoom-0.2.0 → pylocuszoom-0.3.0}/README.md

@@ -33,14 +33,20 @@ Inspired by [LocusZoom](http://locuszoom.org/) and [locuszoomr](https://github.c
 
 ## Installation
 
+```bash
+pip install pylocuszoom
+```
+
+Or with uv:
+
 ```bash
 uv add pylocuszoom
 ```
 
-Or with pip:
+Or with conda (Bioconda):
 
 ```bash
-pip install pylocuszoom
+conda install -c bioconda pylocuszoom
 ```
 
 ## Quick Start
@@ -123,20 +129,30 @@ fig = plotter.plot(
 )
 ```
 
-## Interactive Backends (Coming Soon)
+## Backends
 
-> **Note:** Interactive backends (plotly, bokeh) are planned but not yet fully integrated. Currently all plots use matplotlib.
+pyLocusZoom supports multiple rendering backends:
 
 ```python
-# Static publication-quality plot (default, currently only supported backend)
-plotter = LocusZoomPlotter(species="canine", backend="matplotlib")
-fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
+# Static publication-quality plot (default)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="matplotlib")
 fig.savefig("plot.png", dpi=150)
+
+# Interactive Plotly (hover tooltips, pan/zoom)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="plotly")
+fig.write_html("plot.html")
+
+# Interactive Bokeh (dashboard-ready)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="bokeh")
 ```
 
-Future releases will support:
-- **Plotly**: Interactive plots with hover tooltips, zoom/pan
-- **Bokeh**: Dashboard-friendly interactive plots
+| Backend | Output | Best For |
+|---------|--------|----------|
+| `matplotlib` | Static PNG/PDF/SVG | Publications, presentations |
+| `plotly` | Interactive HTML | Web reports, data exploration |
+| `bokeh` | Interactive HTML | Dashboards, web apps |
+
+> **Note:** All backends support gene track, recombination overlay, and LD legend. SNP labels (auto-positioned with adjustText) are matplotlib-only.
 
 ## Stacked Plots
 

pylocuszoom-0.3.0/bioconda/meta.yaml

@@ -0,0 +1,54 @@
+{% set name = "pylocuszoom" %}
+{% set version = "0.3.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  sha256: REPLACE_WITH_SHA256_AFTER_PYPI_PUBLISH
+
+build:
+  noarch: python
+  number: 0
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+
+requirements:
+  host:
+    - python >=3.10
+    - pip
+    - hatchling
+  run:
+    - python >=3.10
+    - matplotlib-base >=3.5.0
+    - pandas >=1.4.0
+    - numpy >=1.21.0
+    - loguru >=0.7.0
+    - pyliftover >=0.4
+    - plotly >=5.0.0
+    - bokeh >=3.8.2
+    - python-kaleido >=0.2.0
+    - adjusttext >=0.8
+
+test:
+  imports:
+    - pylocuszoom
+  commands:
+    - python -c "from pylocuszoom import LocusZoomPlotter"
+
+about:
+  home: https://github.com/michael-denyer/pylocuszoom
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  license_file: LICENSE
+  summary: Regional association plots for GWAS results with LD coloring
+  description: |
+    pyLocusZoom creates publication-quality regional association plots
+    for GWAS results with LD coloring, gene tracks, and recombination
+    rate overlays. Supports canine, feline, and custom species.
+  dev_url: https://github.com/michael-denyer/pylocuszoom
+
+extra:
+  recipe-maintainers:
+    - michael-denyer